Devices that convert information from one form into another according to a definite procedure are known as automata. One such hypothetical device is the universal Turing machine, which stimulated work leading to the development of modern computers. The Turing machine and its special cases, including finite automata, operate by scanning a data tape, whose striking analogy to information-encoding biopolymers inspired several designs for molecular DNA computers. Laboratory-scale computing using DNA and human-assisted protocols has been demonstrated, but the realization of computing devices operating autonomously on the molecular scale remains rare. Here we describe a programmable finite automaton comprising DNA and DNA-manipulating enzymes that solves computational problems autonomously. The automaton's hardware consists of a restriction nuclease and ligase, the software and input are encoded by double-stranded DNA, and programming amounts to choosing appropriate software molecules. Upon mixing solutions containing these components, the automaton processes the input molecule via a cascade of restriction, hybridization and ligation cycles, producing a detectable output molecule that encodes the automaton's final state, and thus the computational result. In our implementation 1012 automata sharing the same software run independently and in parallel on inputs (which could, in principle, be distinct) in 120 microl solution at room temperature at a combined rate of 109 transitions per second with a transition fidelity greater than 99.8%, consuming less than 10-10 W.

Low OGG activity is associated with an increased risk of lung cancer. Although prospective studies are needed to validate the results, they suggest that smoking cessation in individuals with reduced OGG activity might be an effective strategy in lung cancer prevention.

Efficient DNA repair mechanisms comprise a critical component in the protection against human cancer, as indicated by the high predisposition to cancer of individuals with germ-line mutations in DNA repair genes. This includes biallelic germ-line mutations in the MUTYH gene, encoding a DNA glycosylase that is involved in the repair of oxidative DNA damage, which strongly predispose humans to a rare hereditary form of colorectal cancer. Extensive research efforts including biochemical, enzymological and genetic studies in model organisms established that the oxidative DNA lesion 8-oxoguanine is mutagenic, and that several DNA repair mechanisms operate to prevent its potentially mutagenic and carcinogenic outcome. Epidemiological studies on the association with sporadic cancers of single nucleotide polymorphisms in genes such as OGG1, involved in the repair of 8-oxoguanine yielded conflicting results, and suggest a minor effect at best. A new approach based on the functional analysis of DNA repair enzymatic activity showed that reduced activity of 8-oxoguanine DNA glycosylase (OGG) is a risk factor in lung and head and neck cancer. Moreover, the combination of smoking and low OGG activity was associated with a higher risk, suggesting a potential strategy for risk assessment and prevention of lung cancer, as well as other types of cancer.

The unique properties of DNA make it a fundamental building block in the fields of supramolecular chemistry, nanotechnology, nano-circuits, molecular switches, molecular devices, and molecular computing. In our recently introduced autonomous molecular automaton, DNA molecules serve as input, output, and software, and the hardware consists of DNA restriction and ligation enzymes using ATP as fuel. In addition to information, DNA stores energy, available on hybridization of complementary strands or hydrolysis of its phosphodiester backbone. Here we show that a single DNA molecule can provide both the input data and all of the necessary fuel for a molecular automaton. Each computational step of the automaton consists of a reversible software molecule͞input molecule hybridization followed by an irreversible software-directed cleavage of the input molecule, which drives the computation forward by increasing entropy and releasing heat. The cleavage uses a hitherto unknown capability of the restriction enzyme FokI, which serves as the hardware, to operate on a noncovalent software͞input hybrid. In the previous automaton, software͞input ligation consumed one software molecule and two ATP molecules per step. As ligation is not performed in this automaton, a fixed amount of software and hardware molecules can, in principle, process any input molecule of any length without external energy supply. Our experiments demonstrate 3 ؋ 10 12 automata per l performing 6.6 ؋ 10 10 transitions per second per l with transition fidelity of 99.9%, dissipating about 5 ؋ 10 ؊9 W͞ l as heat at ambient temperature.

In this work we have demonstrated the complex LET dependence of clustered-lesion yields, governed by interplay of the radical recombination and change in track structure. As expected, there was also a significant difference in clustered lesion yields between various radiation fields, having the same or similar LET values, but differing in nanometric track structure.

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An increasing number of studies indicate that reduced DNArepair capacity is associated with increased cancer risk. Using a functional assay for the removal of the oxidative DNA lesion 8-oxoguanine by the DNA-repair enzyme 8-oxoguanine DNA glycosylase 1 (OGG1), we have previously shown that reduced OGG activity is a risk factor in lung cancer. Here, we report that OGG activity in peripheral blood mononuclear cells from 37 cases with squamous cell carcinoma of the head and neck (SCCHN) was significantly lower than in 93 control subjects, frequency matched for age and gender. Retesting of OGG activity 3 to 4 years after diagnosis and successful treatment of 18 individuals who recovered from the disease showed that OGG activity values were similar to those determined at diagnosis, suggesting that reduced OGG activity in case patients was not caused by the disease. Logistic regression analysis indicated that the adjusted odds ratio (OR) associated with a unit decrease in OGG activity was statistically significantly increased [OR, 2.3; 95% confidence interval (95% CI), 1.5-3.4]. Individuals in the lowest tertile of OGG activity exhibited an increased risk of SCCHN with an OR of 7.0 (95% CI, 2.0-24.5). The combination of smoking and low OGG was associated with a highly increased estimated relative risk for SCCHN. These results suggest that low OGG is associated with the risk of SCCHN, and if confirmed by additional epidemiologic studies, screening of smokers for low OGG activity might be used as a strategy for the prevention of lung cancer and SCCHN. (Cancer Res 2006; 66(24): 11683-9)

Bypass synthesis by DNA polymerase II was studied using a synthetic 40-nucleotide-long gapped duplex DNA containing a site-specific abasic site analog, as a model system for mutagenesis associated with DNA lesions. Bypass synthesis involved a rapid polymerization step terminating opposite the nucleotide preceding the lesion, followed by a slow bypass step. Bypass was found to be dependent on polymerase and dNTP concentrations, on the DNA sequence context, and on the size of the gap. The key step in induced mutagenesis is believed to be the insertion of a nucleotide opposite a DNA lesion by a DNA polymerase, a reaction termed bypass or translesion DNA synthesis (reviewed in Refs. 1 and 2). Due to the incorrect coding information of most DNA lesions, such a reaction is potentially mutagenic. In the bacterium Escherichia coli, induced mutagenesis by a variety of DNA-damaging agents was found to be dependent on particular gene products in addition to the polymerase, i.e. the UmuD, UmuC, and RecA proteins (1, 2). The fact that the expression of these proteins is under the regulation of the SOS stress response suggested that induced mutagenesis is a regulated process, which cannot occur without these SOS proteins (1, 2).Early experiments clearly demonstrated that DNA lesions arrest DNA synthesis by a variety of DNA polymerases (3, 4), suggesting that bypass synthesis cannot occur without the UmuD, UmuC, and RecA proteins. However, a growing body of literature documents the ability of a variety of purified DNA polymerases to polymerize through DNA lesions unassisted by other proteins (5-16). Using a cell-free assay system for UV mutagenesis, we have demonstrated that crude protein extracts (17, 18) or a reconstituted system consisting of six purified proteins (19) can promote UV mutagenesis in vitro in the absence of RecA, UmuD, and UmuC. These observations create an apparent paradox; in vitro DNA polymerases can bypass lesions and produce mutations in the absence of UmuD, UmuC, and RecA, but in vivo these proteins are required in most mutagenesis assay systems. Notably, there are two exceptions, where pathways of UV mutagenesis were reported to be independent on the Umu proteins: in phage S13 (20) and in the F factor (21).Very little is known on the ability of DNA polymerase II (pol II) 1 (22, 23) to bypass DNA lesions (11). Polymerase II is UVinducible, and its gene is 25). The in vivo role of pol II was unknown for many years, and only recently have several studies suggested roles for pol II in adaptive mutagenesis (26,27), in response to oxidative damage (26), and in bypass of abasic sites in vivo (28). Our recent finding that pol III core and pol II can each function to promote UV mutations in an in vitro system reconstituted from purified components (19) prompted us to study translesion DNA synthesis by purified DNA polymerase II. Here we describe the analysis of bypass synthesis by DNA polymerase II, and provide a side-byside comparison of bypass by the three DNA polymerases of E. coli: DNA polymerases I, II, an...